Distinct layers of iron(III) and manganese(IV) (Fe/Mn) oxides are found buried within the reducing part of the sediments in Lake Baikal and cause considerable complexity and steep vertical gradients with respect to the redox sequence. For the on-site investigation of the responsible biogeochemical processes, we applied filter tube samplers for the extraction of sediment porewater combined with a portable capillary electrophoresis instrument for the analyses of inorganic cations and anions. On the basis of the new results, the sequence of diagenetic processes leading to the formation, transformation, and dissolution of the Fe/Mn layers was investigated. With two exemplary cores we demonstrate that the dissolution of particulate Fe and Mn is coupled to the anaerobic oxidation of CH₄ (AOM) either via the reduction of sulphate (SO₄²⁻) and the subsequent generation of Fe(II) by S(−II) oxidation, or directly coupled to Fe reduction. Dissolved Fe(II) diffuses upwards to reduce particulate Mn(IV) thus forming a sharp mineral boundary. An alternative dissolution pathway is indicated by the occurrence of anaerobic nitrification of NH₄⁺ observed at locations with Mn(IV). Furthermore, the reasons and consequences of the non-steady-state sediment pattern and the resulting redox discontinuities are discussed and a suggestion for the burial of active Fe/Mn layers is presented.